I would like to use the IoT pHAT with the RPi3, simply to use it’s u.FL connector with an external antenna. Has anybody tested this? If so, how can we make sure that Raspbian is using the appropriate chip?

yes it’s working but there is then just one Wlan interface the internal one will be deactivated.
That’s the problem i’m running into in the moment. I just got an fresh Pi Zero with Wlan and if i plug the IoT pHAT in the internal Wlan Interface isn’t existing anymore. Same with the Pi3 always just one Wlan0 instead of two.

This is because the Pi has a grand total of one SDIO interface, and it can either be used by the onboard wifi, or a device attached to the GPIO pins, there’s no way for it to be able to talk to two SDIO devices at once, much like how you can’t stuff two SD cards into the slot on the pi at once.